DNA-binding small molecules are widespread in the cell and heavily used in
biological applications. Here, we use magnetic tweezers, which control the force and torque applied to single DNAs, to study three small molecules:
ethidium bromide (EtBr), a well-known
intercalator;
netropsin, a minor-groove binding anti-microbial
drug; and
topotecan, a clinically used anti-
tumor drug. In the low-force limit in which biologically relevant torques can be accessed (<10 pN), we show that
ethidium intercalation lengthens
DNA ∼1.5-fold and decreases the persistence length, from which we extract binding constants. Using our control of supercoiling, we measure the decrease in
DNA twist per intercalation to be 27.3±1° and demonstrate that
ethidium binding delays the accumulation of torsional stress in
DNA, likely via direct reduction of the torsional modulus and torque-dependent binding. Furthermore, we observe that EtBr stabilizes the
DNA duplex in regimes where bare
DNA undergoes structural transitions. In contrast, minor groove binding by
netropsin affects neither the contour nor persistence length significantly, yet increases the twist per base of
DNA. Finally, we show that
topotecan binding has consequences similar to those of EtBr, providing evidence for an intercalative binding mode. These insights into the torsional consequences of
ligand binding can help elucidate the effects of small-molecule drugs in the cellular environment.